Related papers: Detecting lateral genetic material transfer
Methods of transfer learning try to combine knowledge from several related tasks (or domains) to improve performance on a test task. Inspired by causal methodology, we relax the usual covariate shift assumption and assume that it holds true…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
An 1d model with time-dependent random hopping is proposed to describe charge transport in DNA. It admits to investigate both diffusion of electrons and their tunneling between different sites in DNA. The tunneling appears to be strongly…
Lateral diffusion of molecules on surfaces plays a very important role in various biological processes, including lipid transport across the cell membrane, synaptic transmission and other phenomena such as exo- and endocytosis, signal…
The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed to lateral genetic transfer (LGT) between different strains or species. However, there has been very little study of the extent…
In situ scanning transmission electron microscopy enables observation of the domain dynamics in ferroelectric materials as a function of externally applied bias and temperature. The resultant data sets contain a wealth of information on…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
Strong experimental and theoretical evidence shows that transcription factors and other specific DNA-binding proteins find their sites using a two-mode search: alternating between 3D diffusion through the cell and 1D sliding along the DNA.…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…
For the past few years, deep generative models have increasingly been used in biological research for a variety of tasks. Recently, they have proven to be valuable for uncovering subtle cell phenotypic differences that are not directly…
Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
We explore layered strongly correlated materials as a platform to identify and control unconventional heat transfer phenomena. We demonstrate that these systems can be tailored to sustain a wide spectrum of heat transport regimes, ranging…
Terahertz Time-Domain Spectroscopy is a powerful technique for extracting the low-frequency optical properties of materials. However, the optical constants are difficult to determine directly from the experimental transfer function, such…
In this work we investigate the electronic transport along model DNA molecules using an effective tight-binding approach that includes the backbone on site energies. The localization length and participation number are examined as a…
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of the pi-stacking interaction $b$ sharing a charge between different base pairs and the…
Transfer learning (TL) is used to extrapolate the physics information encoded in a Generative Adversarial Network (GAN) trained on synthetic neutrino-carbon inclusive scattering data to related processes such as neutrino-argon and…
Recent works on localized charge transport along DNA, based on a three--dimensional, tight--binding model (Eur. Phys. J. B 30:211, 2002; Phys. D 180:256, 2003), suggest that charge transport is mediated by the coupling of the radial and…